Identification of hub genes involved in the occurrence and development of hepatocellular carcinoma via bioinformatics analysis.

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Thus, the aim of the present study was to identify the hub genes and underlying pathways of HCC via bioinformatics analyses. The present study screened three datasets, including GSE112790, GSE84402 and GSE74656 from the Gene Expression Omnibus (GEO) database, and downloaded the RNA-sequencing of HCC from The Cancer Genome Atlas (TCGA) database. The differentially expressed genes (DEGs) in both the GEO and TCGA datasets were filtered, and the screened DEGs were subsequently analyzed for functional enrichment pathways. A protein-protein interaction (PPI) network was constructed, and hub genes were further screened to create the Kaplan-Meier curve using cBioPortal. The expression levels of hub genes were then validated in different datasets using the Oncomine database. In addition, associations between expression and tumor grade, hepatitis virus infection status, satellites and vascular invasion were assessed. A total of 126 DEGs were identified, containing 70 upregulated genes and 56 downregulated genes from the GEO and TCGA databases. By constructing the PPI network, the present study identified hub genes, including cyclin B1 (CCNB1), cell-division cycle protein 20 (CDC20), cyclin-dependent kinase 1, BUB1 mitotic checkpoint serine/threonine kinase β (BUB1B), cyclin A2, nucleolar and spindle associated protein 1, ubiquitin-conjugating enzyme E2 C (UBE2C) and ZW10 interactor. Furthermore, upregulated CCNB1, CDC20, BUB1B and UBE2C expression levels indicated worse disease-free and overall survival. Moreover, a meta-analysis of tumor and healthy tissues in the Oncomine database demonstrated that BUB1B and UBE2C were highly expressed in HCC. The present study also analyzed the data of HCC in TCGA database using univariate and multivariate Cox analyses, and demonstrated that BUB1B and UBE2C may be used as independent prognostic factors. In conclusion, the present study identified several genes and the signaling pathways that were associated with tumorigenesis using bioinformatics analyses, which could be potential targets for the diagnosis and treatment of HCC.", "claims": [{"id": "claim-method", "statement": "The clinical data of HCC from TCGA database was then obtained, and the ‘survival’ package (v3.1–8; http://CRAN.R-project.org/package=survival) of R software was used to perform a univariate analysis and construct the multivariable Cox regression models on BUB1B and UBE2C, and other clinicopathological parameters, and calculated hazard ratios and corresponding 95% confidence intervals.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32724412", "locator": "sections[8] \"Selection and analysis of hub genes\" paragraph 3", "quote": "The clinical data of HCC from TCGA database was then obtained, and the ‘survival’ package (v3.1–8; http://CRAN.R-project.org/package=survival) of R software was used to perform a univariate analysis and construct the multivariable Cox regression models on BUB1B and UBE2C, and other clinicopathological parameters, and calculated hazard ratios and corresponding 95% confidence intervals."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets analyzed during the present study are available in the GEO (https://www.ncbi.nlm.nih.gov/geo/) and TCGA repositories (https://cancergenome.nih.gov/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32724412", "locator": "sections[21] \"Availability of data and materials\" paragraph 2", "quote": "The datasets analyzed during the present study are available in the GEO (https://www.ncbi.nlm.nih.gov/geo/) and TCGA repositories (https://cancergenome.nih.gov/)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:32724412"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. 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